Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

Exploration and Enrichment Analysis of the QTLome for Important Traits in Livestock Species

Background: Quantitative trait loci (QTL) are genomic regions that influence essential traits in livestock. Understanding QTL distribution and density across species' genomes is crucial for animal genetics research. Objectives: This study explored the QTLome of cattle, pigs, sheep, and chickens by analyzing QTL distribution and evaluating the correlation between QTL, gene density, and chromosome size with the aim to identify QTL-enriched genomic regions. Methods: Data from 211,715 QTL (1994-2021) were retrieved from the AnimalQTLdb and analyzed using R software v4.2.1. Unique QTL annotations were identified, and redundant or inconsistent data were removed. Statistical analyses included Pearson correlations and binomial, hypergeometric, and bootstrap-based enrichment tests. Results: QTL densities per Mbp were 10 for bovine, 4 for pig, 1 for sheep, and 3 for chicken genomes. Analysis of QTL distribution across chromosomes revealed uneven patterns, with certain regions enriched for QTL. Correlation analysis revealed a strong positive relationship between QTL and gene density/chromosome size across all species (p < 0.05). Enrichment analysis identified pleiotropic regions, where QTL affect multiple traits, often aligning with known candidate and major genes. Significant QTL-enriched windows (p < 0.05) were detected, with 699 (187), 355 (68), 50 (15), and 38 (17) genomic windows for cattle, pigs, sheep, and chickens, respectively, associated with overall traits (and specific phenotypic categories). Conclusions: This study provides critical insights into QTL distribution and its correlation with gene density, offering valuable data for advancing genetic research in livestock species. The identification of QTL-enriched regions also highlights key areas for future exploration in trait improvement programs.

Comparative transcriptome analysis of T lymphocyte subpopulations and identification of critical regulators defining porcine thymocyte identity

Introduction

The development and migration of T cells in the thymus and peripheral tissues are crucial for maintaining adaptive immunity in mammals. However, the regulatory mechanisms underlying T cell development and thymocyte identity formation in pigs remain largely underexplored.

Method

Here, by integrating bulk and single-cell RNA-sequencing data, we investigated regulatory signatures of porcine thymus and lymph node T cells.

Results

The comparison of T cell subpopulations derived from porcine thymus and lymph nodes revealed that their transcriptomic differences were influenced more by tissue origin than by T cell phenotypes, and that lymph node cells exhibited greater transcriptional diversity than thymocytes. Through weighted gene co-expression network analysis (WGCNA), we identified the key modules and candidate hub genes regulating the heterogeneity of T cell subpopulations. Further, we integrated the porcine thymocyte dataset with peripheral blood mononuclear cell (PBMC) dataset to systematically compare transcriptomic differences between T cell types from different tissues. Based on single-cell datasets, we further identified the key transcription factors (TFs) responsible for maintaining porcine thymocyte identity and unveiled that these TFs coordinately regulated the entire T cell development process. Finally, we performed GWAS of cell type-specific differentially expressed genes (DEGs) and 30 complex traits, and found that the DEGs in thymus-related and peripheral blood-related cell types, especially CD4_SP cluster and CD8-related cluster, were significantly associated with pig productive and reproductive traits.

Discussion

Our findings provide an insight into T cell development and lay a foundation for further exploring the porcine immune system and genetic mechanisms underlying complex traits in pigs.

Pleiotropic architectures of porcine immune and growth trait pairs revealed by a self-product-based transcriptome method

Pleiotropy is an important biological phenomenon with complicated genetic architectures for multiple traits. To date, pleiotropy has been mainly identified by multi-trait genome-wide association studies, but this method has its disadvantages, and new developments for pleiotropy detection methods are needed. Here we define a novel metric, self-product, to measure individual-level co-variation of two traits, and develop a novel self-product-based transcriptome method to detect pleiotropic genes (PGs). Our method was tested using four immune-growth trait pairs and four immune-immune trait pairs in pigs. Comparative transcriptome analyses identified hundreds of candidate PGs related to eight trait pairs from two tails of self-product distribution. Gene Ontology enrichment analysis indicated that most of identified PGs were involved in immune- or growth-related biological processes. We established PG interaction networks to exhibit core genes shared by eight trait pairs, of which CCL5 and IL-10 genes were the hub genes. Genetic association analyses showed that SmaI-polymorphisms of CCL5 and IL-10 genes had significant associations with phenotypic co-variations of multiple trait pairs, indicating that the variants in pleiotropic genes were also pleiotropic variants. Taken together, the validity of our proposed method was preliminarily verified, and our findings provide new insights into the genetic basis of pleiotropic architectures of immune and growth trait pairs in pigs.

Direct-Maternal Genetic Parameters for Litter Size and Body Weight of Piglets of a New Black Breed for the Taiwan Black Hog Market

The objective of this study was to estimate the genetic parameters of litter size and piglet weight from farrowing to weaning in KHAPS Black sows. The genetic parameters investigated were the direct (h²_d), maternal (h²_m), realized (h²_r), and total (h²_T) heritability, as well as correlations (r_d, r_m, and r_dm) within and between traits. The analyses were performed using single- and three-trait animal models with and without maternal genetic effects. In the three-trait model with maternal genetic effect, all estimates of h²_d and h²_m were significantly different from zero except the h²_d of mean birth weight. Positive values of r_d and r_m between traits were observed as expected in the range of 0.322-1.000. Negative values of r_dm were found within and between traits and were less associated with mean piglet weight traits than litter size traits. Estimates of h²_T were consistently larger than those of h²_r in both the single- and three-trait model analyses. In addition, the three-trait model can take into account the association between the traits, so the estimates are more accurate with smaller SEs. In conclusion, maternal genetic effects were not negligible in this study, and thus, a multiple-trait animal model with maternal genetic effects and full pedigree is recommended to assist future pig breeding decisions in this new breed.

Genome-wide association studies for production, respiratory disease, and immune-related traits in Landrace pigs

Identification of a quantitative trait locus (QTL) related to a chronic respiratory disease such as Mycoplasmal pneumonia of swine (MPS) and immune-related traits is important for the genetic improvement of disease resistance in pigs. The objective of this study was to detect a novel QTL for a total of 22 production, respiratory disease, and immune-related traits in Landrace pigs. A total of 874 Landrace purebred pigs, which were selected based on MPS resistance, were genotyped using the Illumina PorcineSNP60 BeadChip. We performed single nucleotide polymorphism (SNP)-based and haplotype-based genome-wide association studies (GWAS) to detect a novel QTL and to evaluate the possibility of a pleiotropic QTL for these traits. SNP-based GWAS detected a total of six significant regions in backfat thickness, ratio of granular leucocytes to lymphatic cells, plasma concentration of cortisol at different ages, and complement alternative pathway activity in serum. The significant region detected by haplotype-based GWAS was overlapped across the region detected by SNP-based GWAS. Most of these detected QTL regions were novel regions with some candidate genes located in them. With regard to a pleiotropic QTL among traits, only three of these detected QTL regions overlapped among traits, and many detected regions independently affected the traits.

Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed

The Jiangquhai (JQ) pig breed is one of the most widely recognized pig populations in China due to its unique and dominant characteristics. In this study, we examined the extent of Linkage disequilibrium (LD) and haplotype block structure of the JQ pig breed, and scanned the blocks for possible genes underlying important QTLs that could either be responsible for some adaptive features in these pigs or might have undergone some selection pressure. We compared some of our results with other Chinese and Western pig breeds. The results show that the JQ breed had the highest total block length (349.73 Mb ≈ 15% of its genome), and the coverage rate of blocks in most of its chromosomes was larger than those of other breeds except for Sus scrofa chromosome 4 (SSC4), SSC6, SSC7, SSC8, SSC10, SSC12, SSC13, SSC14, SSC17, SSC18, and SSCX. Moreover, the JQ breed had more SNPs that were clustered into haplotype blocks than the other breeds examined in this study. Our shared and unique haplotype block analysis revealed that the Hongdenglong (HD) breed had the lowest percentage of shared haplotype blocks while the Shanzhu (SZ) breed had the highest. We found that the JQ breed had an average r² > 0.2 at SNPs distances 10–20 kb and concluded that about 120,000–240,000 SNPs would be needed for a successful GWAS in the breed. Finally, we detected a total of 88 genes harbored by selected haplotype blocks in the JQ breed, of which only 4 were significantly enriched (p-value ≤ 0.05). These genes were significantly enriched in 2 GO terms (p-value < 0.01), and 2 KEGG pathways (p-value < 0.02). Most of these enriched genes were related to health. Also, most of the overlapping QTLs detected in the haplotype blocks were related to meat and carcass quality, as well as health, with a few of them relating to reproduction and production. These results provide insights into the genetic architecture of some adaptive and meat quality traits observed in the JQ pig breed and also revealed the pattern of LD in the genome of the pig. Our result provides significant guidance for improving the statistical power of GWAS and optimizing the conservation strategy for this JQ pig breed.

Selection signature reveals genes associated with susceptibility loci affecting respiratory disease due to pleiotropic and hitchhiking effect in Chinese indigenous pigs

BACKGROUND

Porcine respiratory disease is one of the most important health problems which causes significant economic losses.

OBJECTIVE

To understand the genetic basis for susceptibility to swine enzootic pneumonia (EP) in pigs, we detected 102,809 SNPs in a total of 249 individuals based on genome-wide sequencing data.

METHODS

Genome comparison of three susceptibility to swine EP pig breeds (Jinhua, Erhualian and Meishan) with two western lines that are considered more resistant (Duroc and Landrace) using XP-EHH and FST statistical approaches identified 691 positively selected genes. Based on QTLs, GO terms and literature search, we selected 14 candidate genes that have convincible biological functions associated with swine EP or human asthma.

RESULTS

Most of these genes were tested by several methods including transcription analysis and candidated genes association study. Among these genes: CYP1A1 and CTNNB1 are involved in fertility; TGFBR3 plays a role in meat quality traits; WNT2, CTNNB1 and TCF7 take part in adipogenesis and fat deposition simultaneously; PLAUR (completely linked to AXL, r2=1) plays an essential role in the successful ovulation of matured oocytes in pigs; CLPSL2 (strongly linked to SPDEF, r2=0.848) is involved in male fertility.

CONCLUSION

These adverse genes susceptible to swine EP may be selected while selecting for economic traits (especially reproduction traits) due to pleiotropic and hitchhiking effect of linked genes. Our study provided a completely new point of view to understand the genetic basis for susceptibility or resistance to swine EP in pigs thereby, provide insight for designing sustainable breed selection programs. Finally, the candidate genes are crucial due to their potential roles in respiratory diseases in a large number of species, including human.

Exploring the Genetic Correlation Between Growth and Immunity Based on Summary Statistics of Genome-Wide Association Studies

The relationship between growth and immune phenotypes has been presented in the context of physiology and energy allocation theory, but has rarely been explained genetically in humans. As more summary statistics of genome-wide association studies (GWAS) become available, it is increasingly possible to explore the genetic relationship between traits at the level of genome-wide summary statistics. In this study, publicly available summary statistics of growth and immune related traits were used to evaluate the genetic correlation coefficients between immune and growth traits, as well as the cause and effect relationship between them. In addition, pleiotropic variants and KEGG pathways were identified. As a result, we found negative correlations between birthweight and immune cell count phenotypes, a positive correlation between childhood head circumference and eosinophil counts (EO), and positive or negative correlations between childhood body mass index and immune phenotypes. Statistically significant negative effects of immune cell count phenotypes on human height, and a slight but significant negative influence of human height on allergic disease were also observed. A total of 98 genomic regions were identified as containing variants potentially related to both immunity and growth. Some variants, such as rs3184504 located in SH2B3, rs13107325 in SLC39A8, and rs1260326 located in GCKR, which have been identified to be pleiotropic SNPs among other traits, were found to also be related to growth and immune traits in this study. Meanwhile, the most frequent overlapping KEGG pathways between growth and immune phenotypes were autoimmune related pathways. Pleiotropic pathways such as the adipocytokine signaling pathway and JAK-STAT signaling pathway were also identified to be significant. The results of this study indicate the complex genetic relationship between growth and immune phenotypes, and reveal the genetic background of their correlation in the context of pleiotropy.

A genome scan for selection signatures in Taihu pig breeds using next-generation sequencing

Taihu pig breeds are the most prolific breeds of swine in the world, and they also have superior economic traits, including high resistance to disease, superior meat quality, high resistance to crude feed and a docile temperament. The formation of these phenotypic characteristics is largely a result of long-term artificial or natural selection. Therefore, exploring selection signatures in the genomes of the Taihu pigs will help us to identify porcine genes related to productivity traits, disease and behaviour. In this study, we used both intra-population (Relative Extend Haplotype Homozygosity Test (REHH)) and inter-population (the Cross-Population Extend Haplotype Homozygosity Test (XPEHH); F-STATISTICS, F ST ) methods to detect genomic regions that might be under selection process in Taihu pig breeds. As a result, we found 282 (REHH) and 112 (XPEHH) selection signature candidate regions corresponding to 159.78 Mb (6.15%) and 62.29 Mb (2.40%) genomic regions, respectively. Further investigations of the selection candidate regions revealed that many genes under these genomic regions were related to reproductive traits (such as the TLR9 gene), coat colour (such as the KIT gene) and fat metabolism (such as the CPT1A and MAML3 genes). Furthermore, gene enrichment analyses showed that genes under the selection candidate regions were significantly over-represented in pathways related to diseases, such as autoimmune thyroid and asthma diseases. In conclusion, several candidate genes potentially under positive selection were involved in characteristics of Taihu pig. These results will further allow us to better understand the mechanisms of selection in pig breeding.

Genetic Architecture and Selection of Chinese Cattle Revealed by Whole Genome Resequencing

The bovine genetic resources in China are diverse, but their value and potential are yet to be discovered. To determine the genetic diversity and population structure of Chinese cattle, we analyzed the whole genomes of 46 cattle from six phenotypically and geographically representative Chinese cattle breeds, together with 18 Red Angus cattle genomes, 11 Japanese black cattle genomes and taurine and indicine genomes available from previous studies. Our results showed that Chinese cattle originated from hybridization between Bos taurus and Bos indicus. Moreover, we found that the level of genetic variation in Chinese cattle depends upon the degree of indicine content. We also discovered many potential selective sweep regions associated with domestication related to breed-specific characteristics, with selective sweep regions including genes associated with coat color (ERCC2, MC1R, ZBTB17, and MAP2K1), dairy traits (NCAPG, MAPK7, FST, ITFG1, SETMAR, PAG1, CSN3, and RPL37A), and meat production/quality traits (such as BBS2, R3HDM1, IGFBP2, IGFBP5, MYH9, MYH4, and MC5R). These findings substantially expand the catalogue of genetic variants in cattle and reveal new insights into the evolutionary history and domestication traits of Chinese cattle.

Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data

In this study, we investigated the genetic variants, including SNPs and indels (short insertions or deletions, less than 50 bp in length), in the genomes and genetic structures of five pig populations (in the northern Taihu Lake region, Jiangsu Province) using the genotyping by genome reducing and sequencing (GGRS) approach. A total of 581 million good reads with an average depth of 11× and an average coverage of 2.16% were used to call variants. In general, 202 106 SNPs and 34 415 indels were obtained, of which 2690 SNPs and 224 indels were capable of inducing protein‐coding changes. The genes containing these variants were extracted for functional annotation. The results of gene enrichment analysis revealed that the SNPs under investigation may be associated with reproduction, disease resistance, meat quality and adipose tissue traits, whereas the indels were associated mainly with adipose tissue and disease. Analysis of the genetic structure showed that each population displayed comparable, large differentiations from the others, indicating their uniqueness. In conclusion, the results of our study provide the first genomic overview of the genetic variants and population structures of five Chinese indigenous pig populations.

Pudong White pig: a unique genetic resource disclosed by sequencing data

Pudong White (PW) pigs are distributed in the Taihu region of China and are characterized by their completely white coats. A heated debate concerning this genetic resource and its relationship to Taihu and western pig breeds has arisen, due to the white coat of the animals. To determine whether PW is a unique genetic resource, we performed a detailed assessment of the genetic relationships among PW, six breeds from the Taihu population and three western pig breeds, based on whole-genome single nucleotide polymorphism (SNP) data. A total of 68 102 SNPs were identified in the genomes of the tested populations by next-generation sequencing technology, of which, 64 were determined as the potentially specific to PW breed. The genetic distance between PW pigs and the Taihu population was shorter than that between PW and western breeds. The genetic distance within the PW population was small and neighbour-joining tree analysis revealed that all PW individuals clustered into a separated group, indicating a close genetic relationship among PW individuals which may result from a small effective population size (N e ) and inbreeding. The results of both principal component analysis and evaluation using fastSTRUCTURE demonstrated that PW was clearly differentiated from other breeds. Together, these results indicate that PW is a distinctive genetic resource with a unique genetic structure separate from other Taihu and western pig breeds. Furthermore, this genome-wide comprehensive survey of the relationships among PW, Taihu and western pig breeds, demonstrates the rationality of the current breed classification of PW. The results also provide evidence about the unique genetic resource of PW, based on genome-wide genetic markers. These data will improve our understanding of the genetic structure and current state of PW breed, and facilitate the development of a national project for the conservation and utilization of these pigs.